Plorts despawn over time, placing it there allowed the despawn timer to continue as it was in a loaded section of the map, Though sounds more like you have a case of loading errors for positions so it set the plort under ground. Makes more sense for the later for 2 reasons, one being the changes from the upgrade and the second is the fact the timer I think should have paused.

Same username as I have on discord. I do no damage challenges if you have ideas for those feel free to share